If I connect the usb satellites are acquired and I get a gps lock as soon as I connect the battery all satellite links are lost and the blue led on the controller goes out. Disconnect battery and usb and re boot mission planner and reconnect usb then satellites are acquired again. This is the same whether jp1 is fitted or removed

Hmm, that does sound like something is not quite right as it seems your board is not powering the GPS module when its connected via battery. Are you powering your APM via an ESC or directly via the power module? Also I assume you see all the LED's flashing on your APM when the USB is disconnected and the battery is connected?

Hi Alex, power through power module only, positive and earth cables not connected to the output s, only the signal cable from the esc, I have borrowed a gps module from a fellow flyer and it locates satellites no matter whether power coming from power module or from usb or both. I have notice if line voltage drops to around 7.6v the gps will work however if voltage gets to 7.8v it stops. Noticed this when I attached the fvp transmitter which was bring the voltage down. My friends functioning gps leads me to believe there is a problem with the gps module